Table 4 Multivariate LASSO analysis.

From: Whole genome sequencing of metastatic colorectal cancer reveals prior treatment effects and specific metastasis features

Type

Item

All treatments

Oxaliplatin containing

PLAT/PYR

Target-mono

TOP/PYR

Clinical

Prior Treatment

0.57

    

Gender

 

0.77

 

−1.14

−1.10

Counts

nr of Tandem Duplications

   

1.19

 

nr of 10kb–1Mb deletions

0.01

    

Mutational Signatures

DBS2

−0.02

    

DBS5

0.13

    

DBS11

−0.03

    

SBS17b

0.07

0.13

   

SBS39

0.04

    

SBS41

  

−0.21

  

Driver Genes

APC

0.23

    

KRAS

0.78

    

PIK3CA

0.22

    

FBXW7

   

17.65

 

Non-coding

LINC00672

0.90

    

GISTIC Regions

Gain 17q12

(ERBB2*)

0.44

    

Gain 18p11.32

(CETN1*)

0.59

    

Gain 20q11.1

(BCL2L1*)

0.12

    

Gain 8p11.21

(KAT6A)

 

−0.78

−1.56

  

Gain 7p21.3

(VWDE)

    

3.68

Gain 7q31.2

(MET*)

    

3.59

Gain 7p12.3

(PKD1L1)

    

3.04

Gain 7q34

(no genes in peak)

    

3.59

Gain 14q23.1

(no genes in peak)

    

1.64

Loss 18q12.2

(hsa-mir-924*)

 

−1.52

−3.30

2.79

 

Loss 6q26

(PARK2)

  

−1.38

  

Loss 9p21.3

(CDKN2A*)

  

−1.88

  

Loss 16q23.1

(WWOX)

  

−1.70

  

Loss 4q22.1

(CCSER1)

   

2.66

 

Loss 4q35.1

(IRF2)

   

1.78

 

Loss 18q21.2

(SMAD4)

 

−1.35

−3.30

2.79

 

Loss 18q23

(NFATC1*)

 

−1.14

−3.30

  

Loss Xp22.31

(STS*)

   

−1.40

1.78

Loss 14q23.3

(GPHN)

    

−2.09

  1. Items that reached univariate statistical significance (p < 0.05) were used in a multivariable penalized ordinal regression model for treatment response. Univariate regression was performed for genomic features (Supplementary Data 3) using the ‘polr’ function from the MASS R package (v7.3-51.4) and subsequently those with a univariate two-sided p-value <0.05 were selected for multivariable ordered LASSO regression using the ordinalNet R package (v2.7). Regression coefficients are shown for features that remained significant in the multivariable model.
  2. *Multiple genes present in region; bold: known Fragile Site region
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